Alignments for a candidate for astB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for astB in Shewanella loihica PV-4

Align Succinylarginine dihydrolase (EC 3.5.3.23) (characterized)
to candidate 5209772 Shew_2225 succinylarginine dihydrolase (RefSeq)

Query= reanno::ANA3:7024550
         (444 letters)



>FitnessBrowser__PV4:5209772
          Length = 445

 Score =  756 bits (1953), Expect = 0.0
 Identities = 371/445 (83%), Positives = 406/445 (91%), Gaps = 1/445 (0%)

Query: 1   MKHFEANFDGLVGPTHNYAGLSFGNVASLNNAALVSNPKAAAKQGLQKAKALADLGMIQG 60
           MKH+EANFDGLVGPTHNYAGLS+GNVASLNNAA +S+PKAAAKQGL+KAKALADLG+ QG
Sbjct: 1   MKHYEANFDGLVGPTHNYAGLSYGNVASLNNAAAISSPKAAAKQGLKKAKALADLGLAQG 60

Query: 61  MLAPQERPDLNTLRRIGFSGSDAQVLQQAAKTAPALLNACCSASSMWTANAATVSPSADT 120
           MLAPQERPDL+TLRRIGFSG+DA+VL +AAK APALL ACCSASSMWTANAATVSPSADT
Sbjct: 61  MLAPQERPDLHTLRRIGFSGTDAEVLNKAAKQAPALLRACCSASSMWTANAATVSPSADT 120

Query: 121 RDGKLHFTPANLVDKLHRSIEPTTTGRILTATFNDPHYFHHHNHLPEHNSFGDEGAANHT 180
            DGK+HFTPANLVDKLHRSIEP TTG IL ATFN+  YFHHH HLPEH SFGDEGAANHT
Sbjct: 121 HDGKIHFTPANLVDKLHRSIEPVTTGNILAATFNNSRYFHHHQHLPEHVSFGDEGAANHT 180

Query: 181 RLCQEYGHAGVELFVYGQEATNPNAPRPQKYPARQTLEASMAIARLHQLEEDNCVFIQQN 240
           RLC EYGHAG+ELFVYGQEATNPNAP+P+KYPARQTLEAS AIARLHQL++++ VFIQQN
Sbjct: 181 RLCSEYGHAGIELFVYGQEATNPNAPKPKKYPARQTLEASQAIARLHQLDDESSVFIQQN 240

Query: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFLNTQAKLDEIRRKLD-TELFFIEVPTTKVAI 299
           PDVIDQGVFHNDVIAVGNQNVLFYHEQAF++TQ KL EI+ K +  EL FIEVPT KV I
Sbjct: 241 PDVIDQGVFHNDVIAVGNQNVLFYHEQAFVDTQKKLAEIQDKFNGKELHFIEVPTAKVGI 300

Query: 300 NNAVKSYLFNTQIITLPSGEMAIIAPTDCQENPAVYAYLNELLTLNTPIKQVLYFDVKQS 359
            +AVKSYLFNTQI+TLP+GEMAIIAPT+CQEN AVYAYLNEL+TL TPIKQV YFDVKQS
Sbjct: 301 QDAVKSYLFNTQIVTLPNGEMAIIAPTNCQENEAVYAYLNELVTLGTPIKQVHYFDVKQS 360

Query: 360 MQNGGGPACLRLRVAMNEREVAAANQHTLLNDALFARLNTWVDKHYRDRLSTQDLADPQL 419
           MQNGGGPACLRLRVAMNE E+AA N +TL+ND LF RLN WV+KHYRD L+  DLADPQL
Sbjct: 361 MQNGGGPACLRLRVAMNETELAAVNPNTLMNDELFNRLNLWVEKHYRDELAIDDLADPQL 420

Query: 420 VVESRTALDELTQIMKLGSVYPFQR 444
           +VESRTALDELTQIMKLGSVY FQ+
Sbjct: 421 IVESRTALDELTQIMKLGSVYQFQK 445


Lambda     K      H
   0.318    0.132    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 728
Number of extensions: 15
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 444
Length of database: 445
Length adjustment: 32
Effective length of query: 412
Effective length of database: 413
Effective search space:   170156
Effective search space used:   170156
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 5209772 Shew_2225 (succinylarginine dihydrolase (RefSeq))
to HMM TIGR03241 (astB: succinylarginine dihydrolase (EC 3.5.3.23))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03241.hmm
# target sequence database:        /tmp/gapView.8267.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03241  [M=443]
Accession:   TIGR03241
Description: arg_catab_astB: succinylarginine dihydrolase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.6e-225  734.4   1.8   2.9e-225  734.3   1.8    1.0  1  lcl|FitnessBrowser__PV4:5209772  Shew_2225 succinylarginine dihyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209772  Shew_2225 succinylarginine dihydrolase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.3   1.8  2.9e-225  2.9e-225       2     443 .]       4     444 ..       3     444 .. 0.99

  Alignments for each domain:
  == domain 1  score: 734.3 bits;  conditional E-value: 2.9e-225
                        TIGR03241   2 yevnfdGlvGlthnyaGlsfGnkastsnkksvsnpklaakqGllkmkaladlGfkqgvlapqerpdiaalrklGfsGs 79 
                                      ye+nfdGlvG+thnyaGls+Gn+as +n  ++s pk+aakqGl+k kaladlG++qg+lapqerpd+ +lr++GfsG 
  lcl|FitnessBrowser__PV4:5209772   4 YEANFDGLVGPTHNYAGLSYGNVASLNNAAAISSPKAAAKQGLKKAKALADLGLAQGMLAPQERPDLHTLRRIGFSGT 81 
                                      9***************************************************************************** PP

                        TIGR03241  80 deevlekaareapellsavssassmwtanaatvspsadtadgrvhftaanlnnkfhrsieaettervlkaifadekkf 157
                                      d+evl+kaa++ap ll a +sassmwtanaatvspsadt dg++hft+anl  k+hrsie  tt ++l+a+f++ ++f
  lcl|FitnessBrowser__PV4:5209772  82 DAEVLNKAAKQAPALLRACCSASSMWTANAATVSPSADTHDGKIHFTPANLVDKLHRSIEPVTTGNILAATFNNSRYF 159
                                      ****************************************************************************** PP

                        TIGR03241 158 avhealpavallGdeGaanhtrlgaeydepgvelfvyGraal.erepkpkryparqtleasqavarlhqleeekvvya 234
                                       +h+ lp++ ++GdeGaanhtrl++ey+++g+elfvyG++a   ++pkpk+yparqtleasqa+arlhql++e+ v++
  lcl|FitnessBrowser__PV4:5209772 160 HHHQHLPEHVSFGDEGAANHTRLCSEYGHAGIELFVYGQEATnPNAPKPKKYPARQTLEASQAIARLHQLDDESSVFI 237
                                      ****************************************997899******************************** PP

                        TIGR03241 235 qqnpdvidqGvfhndviavsnrevlfhhekaflnqsqvldelraklaalgqelvaievpdaevsvedavssylfnsql 312
                                      qqnpdvidqGvfhndviav+n++vlf+he+af+++++ l+e++ k++++  el+ ievp+a+v ++dav+sylfn+q+
  lcl|FitnessBrowser__PV4:5209772 238 QQNPDVIDQGVFHNDVIAVGNQNVLFYHEQAFVDTQKKLAEIQDKFNGK--ELHFIEVPTAKVGIQDAVKSYLFNTQI 313
                                      **********************************************988..8999*********************** PP

                        TIGR03241 313 lskedgkmllvvpeecreneavwayldelvaadgpikevkvfdlresmknGGGpaclrlrvvlndaelaavnpkvlls 390
                                      ++  +g+m ++ p +c+eneav+ayl+elv+ ++pik+v+ fd+++sm+nGGGpaclrlrv++n++elaavnp++l++
  lcl|FitnessBrowser__PV4:5209772 314 VTLPNGEMAIIAPTNCQENEAVYAYLNELVTLGTPIKQVHYFDVKQSMQNGGGPACLRLRVAMNETELAAVNPNTLMN 391
                                      ****************************************************************************** PP

                        TIGR03241 391 dalfatlnkwvdrhyrdrlsakdladpqllvesrtaldeltqilnlGsvyefq 443
                                      d+lf++ln wv++hyrd+l+ +dladpql+vesrtaldeltqi++lGsvy+fq
  lcl|FitnessBrowser__PV4:5209772 392 DELFNRLNLWVEKHYRDELAIDDLADPQLIVESRTALDELTQIMKLGSVYQFQ 444
                                      ****************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (445 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.81
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources